Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.8+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.6+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.5+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.3.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.2.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.1.0 |
PrecursorIonSelector |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
openms | 2.8 | package |
openms-thirdparty | 2.8 | package |
omssa | 2.1.9 | package |
blast | 2.13.0 | package |
ctdopts | 1.4 | package |
Additional information about this tool |
#def quote(s): #set $s = [ _ for _ in $s.split(" ") if _ != "" ] #set $q = False #for $i, $p in enumerate($s): #if $p == "": #continue #end if #if $p.startswith('"'): #set $q = True #end if ## #if p.startswith('-'): ## #set p = "\\" + p ## #elif p.startswith('"-'): ## #set p = "\\" + p[1:] ## #end if #if not $q: #set $s[i] = '"%s"' % p #end if #if $p.endswith('"'): #set $q = False #end if #end for #return " ".join($s) #end def #def oms2gxyext(o) #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} #return m[o] #end def #def gxy2omsext(g) #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} #return m[g] #end def #import re ## Preprocessing mkdir in && ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir next_feat && #end if mkdir ids && ln -s '$ids' 'ids/${re.sub("[^\w\-_]", "_", $ids.element_identifier)}.$gxy2omsext($ids.ext)' && #if $raw_data: mkdir raw_data && ln -s '$raw_data' 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)' && #end if #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir sim_results && #end if #if $db_path: mkdir db_path && ln -s '$db_path' 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)' && #end if #if $rt_model: mkdir rt_model && ln -s '$rt_model' 'rt_model/${re.sub("[^\w\-_]", "_", $rt_model.element_identifier)}.$gxy2omsext($rt_model.ext)' && #end if #if $dt_model: mkdir dt_model && ln -s '$dt_model' 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)' && #end if ## Main program call set -o pipefail && PrecursorIonSelector -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' 'PrecursorIonSelector.ctd' '$args_json' '$hardcoded_json' && PrecursorIonSelector -ini PrecursorIonSelector.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out 'out/output.${gxy2omsext("featurexml")}' #end if #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -next_feat 'next_feat/output.${gxy2omsext("featurexml")}' #end if -ids 'ids/${re.sub("[^\w\-_]", "_", $ids.element_identifier)}.$gxy2omsext($ids.ext)' #if $raw_data: -raw_data 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)' #end if #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -sim_results 'sim_results/output.${gxy2omsext("txt")}' #end if #if $db_path: -db_path 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)' #end if #if $rt_model: -rt_model 'rt_model/${re.sub("[^\w\-_]", "_", $rt_model.element_identifier)}.$gxy2omsext($rt_model.ext)' #end if #if $dt_model: -dt_model 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out/output.${gxy2omsext("featurexml")}' '$out' #end if #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'next_feat/output.${gxy2omsext("featurexml")}' '$next_feat' #end if #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'sim_results/output.${gxy2omsext("txt")}' '$sim_results' #end if #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv 'PrecursorIonSelector.ctd' '$ctd_out' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
in: PrecursorIonSelector_features.featureXML ids: PrecursorIonSelector_ids.idXML num_precursors: 1 load_preprocessing: False store_preprocessing: False simulation: True db_path: PrecursorIonSelector_db.fasta fixed_modifications: algorithm|type: IPS algorithm|max_iteration: 10 algorithm|rt_bin_capacity: 10 algorithm|step_size: 1 algorithm|peptide_min_prob: 0.2 algorithm|sequential_spectrum_order: False algorithm|MIPFormulation|thresholds|min_protein_probability: 0.2 algorithm|MIPFormulation|thresholds|min_protein_id_probability: 0.95 algorithm|MIPFormulation|thresholds|min_pt_weight: 0.5 algorithm|MIPFormulation|thresholds|min_mz: 500.0 algorithm|MIPFormulation|thresholds|max_mz: 5000.0 algorithm|MIPFormulation|thresholds|min_pred_pep_prob: 0.5 algorithm|MIPFormulation|thresholds|min_rt_weight: 0.5 algorithm|MIPFormulation|thresholds|use_peptide_rule: True algorithm|MIPFormulation|thresholds|min_peptide_ids: 2 algorithm|MIPFormulation|thresholds|min_peptide_probability: 0.95 algorithm|MIPFormulation|combined_ilp|k1: 0.2 algorithm|MIPFormulation|combined_ilp|k2: 0.2 algorithm|MIPFormulation|combined_ilp|k3: 0.4 algorithm|MIPFormulation|combined_ilp|scale_matching_probs: True algorithm|MIPFormulation|feature_based|no_intensity_normalization: False algorithm|MIPFormulation|feature_based|max_number_precursors_per_feature: 1 algorithm|Preprocessing|precursor_mass_tolerance: 0.9 algorithm|Preprocessing|precursor_mass_tolerance_unit: Da algorithm|Preprocessing|preprocessed_db_path: algorithm|Preprocessing|preprocessed_db_pred_rt_path: algorithm|Preprocessing|preprocessed_db_pred_dt_path: algorithm|Preprocessing|max_peptides_per_run: 100000 algorithm|Preprocessing|missed_cleavages: 1 algorithm|Preprocessing|taxonomy: algorithm|Preprocessing|store_peptide_sequences: False algorithm|Preprocessing|rt_settings|min_rt: 960.0 algorithm|Preprocessing|rt_settings|max_rt: 3840.0 algorithm|Preprocessing|rt_settings|rt_step_size: 30.0 algorithm|Preprocessing|rt_settings|gauss_mean: -1.0 algorithm|Preprocessing|rt_settings|gauss_sigma: 3.0 adv_opts|solver: GLPK adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'sim_results_FLAG'] |
name: value name: value |
PrecursorIonSelector_features.featureXML PrecursorIonSelector_ids.idXML PrecursorIonSelector_db.fasta value |
Test-2 |
in: PrecursorIonSelector_features.featureXML ids: PrecursorIonSelector_ids.idXML num_precursors: 1 load_preprocessing: False store_preprocessing: False simulation: False db_path: PrecursorIonSelector_db.fasta fixed_modifications: algorithm|type: IPS algorithm|max_iteration: 10 algorithm|rt_bin_capacity: 10 algorithm|step_size: 1 algorithm|peptide_min_prob: 0.2 algorithm|sequential_spectrum_order: False algorithm|MIPFormulation|thresholds|min_protein_probability: 0.2 algorithm|MIPFormulation|thresholds|min_protein_id_probability: 0.95 algorithm|MIPFormulation|thresholds|min_pt_weight: 0.5 algorithm|MIPFormulation|thresholds|min_mz: 500.0 algorithm|MIPFormulation|thresholds|max_mz: 5000.0 algorithm|MIPFormulation|thresholds|min_pred_pep_prob: 0.5 algorithm|MIPFormulation|thresholds|min_rt_weight: 0.5 algorithm|MIPFormulation|thresholds|use_peptide_rule: True algorithm|MIPFormulation|thresholds|min_peptide_ids: 2 algorithm|MIPFormulation|thresholds|min_peptide_probability: 0.95 algorithm|MIPFormulation|combined_ilp|k1: 0.2 algorithm|MIPFormulation|combined_ilp|k2: 0.2 algorithm|MIPFormulation|combined_ilp|k3: 0.4 algorithm|MIPFormulation|combined_ilp|scale_matching_probs: True algorithm|MIPFormulation|feature_based|no_intensity_normalization: False algorithm|MIPFormulation|feature_based|max_number_precursors_per_feature: 1 algorithm|Preprocessing|precursor_mass_tolerance: 0.9 algorithm|Preprocessing|precursor_mass_tolerance_unit: Da algorithm|Preprocessing|preprocessed_db_path: algorithm|Preprocessing|preprocessed_db_pred_rt_path: algorithm|Preprocessing|preprocessed_db_pred_dt_path: algorithm|Preprocessing|max_peptides_per_run: 100000 algorithm|Preprocessing|missed_cleavages: 1 algorithm|Preprocessing|taxonomy: algorithm|Preprocessing|store_peptide_sequences: False algorithm|Preprocessing|rt_settings|min_rt: 960.0 algorithm|Preprocessing|rt_settings|max_rt: 3840.0 algorithm|Preprocessing|rt_settings|rt_step_size: 30.0 algorithm|Preprocessing|rt_settings|gauss_mean: -1.0 algorithm|Preprocessing|rt_settings|gauss_sigma: 3.0 adv_opts|solver: GLPK adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG'] |
name: value name: value |
PrecursorIonSelector_features.featureXML PrecursorIonSelector_ids.idXML PrecursorIonSelector_db.fasta value |